Ever since New York Times reporter James Risen received his first subpoena from the Justice Department more than six years ago, occasional news reports have skimmed the surface of a complex story. The usual gloss depicts a conflict between top officials who want to protect classified information and a journalist who wants to protect confidential sources. Meanwhile, Jeffrey Sterling—a former undercover CIA officer now facing charges under the Espionage Act, whom the feds want Risen to identify as his source—is cast as a disgruntled ex-employee in trouble for allegedly spilling the classified beans.

But the standard media narratives about Risen and Sterling have skipped over deep patterns of government retaliation against recalcitrant journalists and whistleblowers. Those patterns are undermining press freedom, precluding the informed consent of the governed and hiding crucial aspects of US foreign policy. The recent announcement of Eric Holder’s resignation as attorney general has come after nearly five years of the Obama administration extending and intensifying the use of the Justice Department for retribution against investigative journalism and whistleblowing.

Official enmity toward Risen had simmered for years before the Bush administration sent him a subpoena on January 24, 2008. Shortly before the 2004 presidential election, Risen and his colleague Eric Lichtblau put together breakthrough reporting on a warrantless domestic-wiretap program. As it sometimes does with stories deemed sensitive for national security, the Times notified the government of its intent to publish. But under strong pressure from White House officials—including some later implicated in the legally suspect program—Times editors delayed the story’s publication for over a year, until December 2005. The coverage won Risen and Lichtblau a Pulitzer Prize for “carefully sourced stories on secret domestic eavesdropping that stirred a national debate.” It was the kind of debate that the people running the US surveillance state had been desperate to avoid.

The belated publication of those stories came just before Risen brought out a book that contained reporting on the wiretap program and several other sinister initiatives under categories like “counterterrorism” and “counterproliferation.” On January 13, 2006, the week after Risen’s book State of War reached the stores, Attorney General Alberto Gonzales told a news conference that an investigation into the Times wiretap stories was under way and that “it’s too early to make decisions regarding whether or not reporters should go to jail.” Though not apparent at the time, facts later emerged to show that Gonzales was implicated in the illegal wiretapping that Risen exposed. (As White House counsel, Gonzales had authorized continued operation of the program after the Justice Department refused to do so.)

It turned out that the Justice Department was not able to prosecute any whistleblower or make legal trouble for any journalist in connection with the wiretap revelations. But as attorney general—an office he assumed in early 2005—Gonzales ran the department as it collected information that would not only jeopardize the confidentiality of Risen’s sources but also impede his ongoing reporting. Risen’s book, a bestseller, included a chapter that became the ostensible reason for the series of subpoenas and legal threats that have been aimed at Risen since George W. Bush began his final year in the Oval Office.

Under Attorney General Eric Holder, President Obama’s Justice Department took up where the Bush DOJ left off. Risen received a second subpoena for grand-jury testimony in late April 2010. As he noted in a mid-2011 affidavit, “It was my reporting, both in The New York Times and my book State of War, that revealed that the Bush Administration had, in all likelihood, violated the law and the United States Constitution by secretly conducting warrantless domestic wiretapping on American citizens.” At the White House and the Justice Department, he remained unforgiven.

Anger at Risen also endured at the CIA, where officials have loathed his way of flipping over their rocks. Former head CIA lawyer John Rizzo singles out Risen for condemnation in a memoir this year, writing that inside the agency “he has had a reputation for being irresponsible and sneaky.” State of War, which depicted the agency’s leadership as inept and dangerous, only stoked that antipathy.

Some high-ranking individuals have been mainstays in the continuation of policies that Risen exposed in his book. John Brennan—President Obama’s former counterterrorism czar and now CIA director—has been at notable cross-purposes with both Risen and Sterling for more than a decade. Brennan was a senior CIA official when the agency rolled out its torture program under Bush, which came under intense public scrutiny after the use of waterboarding was revealed in a May 13, 2004, front-page Times story with Risen as the lead reporter. And Brennan played a key role in the illegal wiretap program, overseeing the production of what personnel in the program called the “scary memos” intended to justify the domestic spying exposed by Risen. (Brennan has since admitted that he relied on intelligence from the CIA’s interrogation programs to develop such memos, and his tenure in that role spanned the period when the CIA used its most extreme torture.)

* * *

As for Sterling, Brennan played a role in his unhappy departure from the CIA a dozen years ago. In 2000, Sterling filed a discrimination complaint within the agency, asserting that he had been denied certain assignments because of his race. (Sterling was one of the CIA’s few African-American officers.) Brennan, as deputy executive director, was involved in rejecting Sterling’s claim. Sterling responded by suing the CIA; he was fired in 2002. The CIA rebuffed a number of settlement offers and then won dismissal of the entire lawsuit in 2004 after claiming that the litigation would expose state secrets.

In early March 2003, Sterling met with two Senate Intelligence Committee staffers to report that Operation Merlin—the CIA’s ill-conceived and bungled effort in 2000 to use a former Russian scientist to pass flawed nuclear-weapons blueprints to Iran—may have helped Iran’s nuclear ambitions. The government concedes that Sterling went through proper channels when he “disclosed classified information” to committee staff. (In court documents, the prosecution has complained that Sterling was unfairly critical of that operation when he spoke to committee staffers.)

The New York Times was even more deferential to government pressure on the Operation Merlin story than it was with its fourteen-month delay of the warrantless wiretap scoop: it never published the Merlin story, which finally reached the public via Risen’s book after remaining bottled up at the paper of record for more than two years. Later, in an affidavit responding to his third subpoena, which was issued on May 23, 2011, Risen said that he included the exposé of Operation Merlin in his book to help prevent another trumped-up war: “I realized that U.S. intelligence on Iran’s supposed weapons of mass destruction was so flawed, and that the information I had was so important, that this was a story that the public had to know about before yet another war was launched.”

Alarm bells had gone off as soon as the National Security Council got a bootlegged copy of State of War before its publication. Frantic skimming of the book alighted on its final chapter, devoted to the highly classified and embarrassing story of Operation Merlin. On the last day of 2005, officials at an emergency White House meeting tried to figure out how to block distribution. “As best anyone could tell, the books were printed in bulk and stacked somewhere in warehouses,” Rizzo’s memoir recalls. “We arrived at a rueful consensus: game over as far as any realistic possibility to keep the book, and the classified information in it, from getting out.”

The leak investigation of Sterling stretched over seven years, from suspicion in 2003 to indictment in 2010. The Justice Department has sought to justify the delay by relying on a McCarthy-era extension of the statutes of limitation associated with charges against him, and by holding Sterling responsible for the publication of Risen’s book chapter rather than for the conversations the two men allegedly had back in 2003.

The US government has been relentless in its pursuit of Risen in the Sterling investigation. Along with serving three subpoenas on the reporter, the DOJ obtained his credit reports, travel records, credit-card records and bank records. “One former official was asked to sign a document stating he was not a confidential source for New York Times reporter James Risen,” ABC News reported in May 2006. And the government appears to have obtained Risen’s phone records without alerting him, as required by DOJ guidelines. In an affidavit, Risen said that a witness who testified to the grand jury investigating the domestic wiretapping story had been shown “copies of telephone records relating to calls made to and from me.”

In its 2011 Domestic Investigations and Operations Guide, the FBI formally authorized the use of national-security letters to obtain the call records of journalists who are witnesses to a crime. (NSLs are secret orders that the FBI can issue with no judicial review. Recipients are prohibited from telling anyone they’ve received such an order.) The FBI has not publicly changed this policy despite the attorney general’s revised guidelines issued last year and touted as protection for the press. The judge in the Sterling case, Leonie Brinkema, even pointed out that the government has never said whether prosecutors have recordings of Sterling’s conversations with Risen, indicating that she may suspect they do.

The way the Justice Department has constructed its legal case against Risen reeks of retaliation. With the rationale of seeking to rule out people other than Sterling as his sources, the government says it wants to make Risen go through the book’s offending chapter—statement by statement—and identify his sources by alias, at least, to indicate when he learned a certain fact. Such a process could implicate other sources. Given the small universe of people who knew about Operation Merlin (at least according to the government’s claims), such an extent of detail would likely identify all of Risen’s sources, regardless of any role Sterling may have had.

Meanwhile, the prosecution claims that Sterling lied about the details of Operation Merlin in order to get the Senate Intelligence Committee as well as Risen interested in the story. According to a government brief in Sterling’s case, “The grand jury specifically found that the defendant provided information to Risen in a false and misleading manner specifically as a means of inducing Risen to write about it, thus severely undercutting any First Amendment protection to be afforded that information.” (The government even claims that Sterling lied about believing that the Merlin scheme might help, rather than hurt, Iran’s nuclear ambitions.) But according to Rizzo’s memoir, the CIA came to very different conclusions about the accuracy of Risen’s reporting on Operation Merlin. The memoir, which went through CIA review and approval before publication, says the CIA’s chief of operations “confirmed that the details largely were all too distressingly accurate and damaging to CIA sources and methods.” In its prosecution of Sterling, the Justice Department is telling a notably different tale.

Legal maneuvers and contradictions aside, the government insists that such strenuous prosecution efforts are all about safeguarding the CIA’s “sources and methods” to collect information and run covert ops. But neither Risen nor Sterling had anything to do with the serious damage to sources and methods in Iran that the CIA actually suffered during the Bush years. Rather than being caused by journalism or whistleblowing, that damage was entirely self-inflicted. In 2004, an officer at the agency’s headquarters in Virginia mistakenly sent data to an agent that “could be used to identify virtually every spy the CIA had inside Iran,” Risen reported in his book. The mistake morphed into spook disaster when it turned out that the supposed CIA agent on the receiving end was a double agent. Wrote Risen: “The agent quickly turned the data over to Iranian security officials, and it enabled them to ‘roll up’ the CIA’s agent network throughout Iran.” But CIA leaders have no interest in acknowledging their Iran-related failures. Instead, they’ve made vague assertions that Sterling and Risen have caused harm. “All too frequently,” Risen points out, “the government claims that publication of certain information will harm national security, when in reality, the government’s real concern is about covering up its own wrongdoing or avoiding embarrassment.”

* * *

The absurd pretense of merely wishing to “protect” classified information certainly didn’t begin with the Obama presidency. While publicly abhorring leaks, every administration in memory has leaked large quantities of classified information to serve its own ends—especially to journalists with a reliable record of propagating these authorized plants. But the customary gap between pretense and reality has grown into a canyon under Obama. While Risen is a high-profile case, there are others—for example, in 2013, when Holder’s DOJ subpoenaed the phone records of twenty phone lines affecting the work of 100 journalists with the Associated Press to find sources for a CIA-related story by Matt Apuzzo and Adam Goldman—thus uncovering a wide array of journalists’ sources under the guise of pursuing the leaker(s) behind one story.

At the same time, the much-ballyhooed option for whistleblowers of going through the “proper” channels has often functioned as a trap, snaring them for later retribution that has included harassment, formal investigations, strong-arm raids on homes and felony prosecutions.

Several months ago, National Security Agency whistleblower Edward Snowden cited the ordeals of two high-ranking NSA executives, William Binney and Thomas Drake, who became whistleblowers within the system. Their cases “showed us that even if you reveal classic waste, fraud and abuse, frivolous spending, things like that, and you take it to Congress, there’s a very good chance the FBI will kick in your door, pull you out of the shower naked at gunpoint in front of your family and ruin your life,” Snowden said. It was Binney, a high-level NSA intelligence official, who had a gun pointed at him in the shower one day in 2007. Drake, an NSA senior executive, was indicted in 2010; he endured years of bogus investigations and prosecution on Espionage Act charges before the case against him collapsed. (For more on these cases, see Tim Shorrock, “Obama’s Crackdown on Whistleblowers,” April 15, 2013.)

The CIA is no more hospitable to whistleblowers—or to reporters who turn their disclosures into scandals. A decade ago, to the growing dismay of top CIA officials, Risen made it clear that he was no garden-variety reporter. His July 6, 2004, front-page Times story, headlined CIA Held Back Iraqi Arms Data, was a stunning account of agency mendacity. Before the March 2003 invasion of Iraq, the CIA had recruited as informants about thirty relatives of Iraqi scientists—and received strong indications that Saddam Hussein’s government no longer had any programs for developing weapons of mass destruction. But the CIA kept mum about those findings, even as the Bush White House continued to proclaim that invading Iraq was necessary due to its purported WMDs.

Eighteen months after breaking that story in the Times, Risen reported on it in more detail in State of War. But the section of the book that caused panic from Langley to the White House Situation Room on the last day of 2005 was the final chapter, about the Merlin operation against Iran, a country the Bush administration had in its gunsights.

Now, almost fifteen years after the CIA gave Iran some obviously flawed nuclear blueprints, Operation Merlin seems a much more suitable topic for Freedom of Information Act illumination than courtroom prosecution. Yet Jeffrey Sterling awaits trial on ten separate felony counts—seven of them under the Espionage Act—for allegedly telling Risen about that CIA operation. If convicted, Sterling could spend decades in prison. “It is a case that we intend to see through to the end,” Holder told a news conference in September.

* * *

For nearly four years, the Obama administration has been on record with the broad claim that whistleblowing to inform the public is apt to be worse than spying to aid a foreign power. In a January 2011 brief against Sterling, the Justice Department declared that his alleged disclosures “may be viewed as more pernicious than the typical espionage case where a spy sells classified information for money.” That stance implicitly views the people of the United States as a potential enemy force to be deprived of key information, and whistleblowers as hostile agents.

To date, the Obama administration has charged nine people with violating the ninety-seven-year-old Espionage Act—far more than all other administrations combined. But those numbers tell only part of the story. In recent years, many whistleblowers have endured Espionage Act investigations and other coercive measures short of actual prosecution. Such legal actions are part of an approach that sees investigative journalism in the national-security realm as a dire threat. The prosecution of Sterling and the pursuit of Risen embody the recognition that truly independent reporting and whistleblowing need each other. In effect, top government officials seem determined to reach a fundamentally antidemocratic goal—the uninformed consent of the governed.

“Enough is enough,” said three-time Pulitzer Prize–winner David Barstow in a recent statement. “The relentless and by all appearances vindictive effort by two administrations to force Jim Risen into betraying his sources has already done substantial and lasting damage to journalism in the United States.”

Barstow, a longtime New York Times reporter, added: “I’ve felt the chill firsthand. Trusted sources in Washington are scared to talk by telephone, or by email, or even to meet for coffee, regardless of whether the subject touches on national security or not. My fellow investigative reporters commiserate about how we’re being forced to act like drug dealers, taking extreme precautions to avoid leaving any digital bread crumbs about where we’ve been and who we’ve met.”

At The Washington Post, Pulitzer Prize winner Dana Priest was no less vehement. “If the U.S. government were so concerned about the information revealed in Jim Risen’s stunning chapter on a now 14-year-old CIA operation against Iran gone wrong, it would have moved quickly to resolve this matter eight years ago when it was first published,” she wrote. “Instead, it seems obvious now that what officials really want is to hold a hammer over the head of a deeply sourced reporter, and others like him who try to hold the government accountable for what it does, even in secret.”

This past May, Eric Holder made a statement that has been often cited since: “As long as I’m attorney general, no reporter who is doing his job is going to go to jail.” Now that Holder has resigned, the phrase “as long as I’m attorney general” has an ominous ring. But in the long run, the more pivotal concern for the First Amendment hinges on what “doing his job” is understood to mean. For the men and women who work with integrity as journalists, the job must include protecting rather than betraying confidential sources. Yet the official position of the Obama administration insists on such betrayal. In a brief to the Supreme Court in April, the Justice Department argued that the government should enforce what it called “the longstanding common-law rule that reporters have no privilege to refuse to provide direct evidence of criminal wrongdoing by confidential sources.”

The Justice Department was quick to present itself as a supporter of the journalists arrested in Ferguson, Missouri, in mid-August. Its public-affairs director tweeted: “DOJ is lucky to have a gutsy reporter like @Ryanjreilly on our beat.” But CNN’s Jake Tapper retorted: “how do you distinguish between the ‘gutsy’ reporters and the one the administration is threatening to put in jail?”

* * *

The legal assault on Risen and the prosecution of Sterling are integral to the escalating siege that targets core values of investigative reporting and public-service whistleblowing—even as Obama continues to tout what he calls “the most transparent administration in history.” An atmosphere of fear inside government has intensified. Too little media attention has gone to scrutinizing the insidious program known as “Insider Threat,” which pressures federal workers to monitor and report fellow employees suspected of ideological or attitudinal deviance. More recently, Director of National Intelligence James Clapper ordered that government employees in a wide range of intelligence-related agencies must get permission before sharing any nonclassified information with journalists. Clapper called for clearance holders to be continually monitored, an order that Senators Charles Grassley and Ron Wyden worry carries particular hazards for whistleblowers.

The administration’s fixation on information control hardly stops with the intelligence agencies. “Day-to-day intimidation of sources is chilling,” said Sally Buzbee, Washington bureau chief of the Associated Press. According to Buzbee, the AP transportation reporter’s sources “say that if they’re caught talking to her, they will be fired. Even if they just give her facts—about safety, for example. Government press officials say their orders are to squelch anything controversial or that makes the administration look bad.”

Recognizing what’s at stake for press freedom, some in the media establishment have decided to speak up for Risen. In August, a petition backing him—with 100,000 signers and support from press-freedom groups and other organizations, including The Nation—was presented to the Justice Department. The petition points out that journalism without confidential sources would be merely a conduit for official stories—“a situation antithetical to the First Amendment.”

But Sterling—whose situation is far more precarious—has received almost no public support. That should change. At the very least, Sterling chose an admirable but hazardous path by going through channels to inform Senate Intelligence Committee staff about Operation Merlin. When announcing his indictment in January 2011, the Justice Department denounced Sterling for his “underlying selfish and vindictive motivations”—an accusation widely reported by news outlets across the country. Not surprisingly, he has had difficulty finding gainful employment as the pretrial legal maneuvers drag on.

* * *

“In the end, whether Risen goes to jail for contempt or not, the last seven years of his battling subpoenas are well-designed to intimidate other investigative reporters,” Pentagon Papers whistleblower Daniel Ellsberg told The Nation. “Likewise, Sterling’s ordeal comes from a strategy to frighten potential whistleblowers, whether he was the source of this leak or not. The aim is to punish troublemakers with harassment, threats, indictments, years in court and likely prison—even if they’ve only gone through official channels to register accusations about their superiors and agency. That is, by the way, a practical warning to would-be whistleblowers who would prefer to ‘follow the rules.’ But in any case, whoever were the actual sources to the press of information about criminal violations of the Fourth Amendment, in the NSA case, or of reckless incompetence, in the CIA case, they did a great public service.”

Such public service is the kind of good deed that rarely goes unpunished. Attorney Jesselyn Radack, who directs the program on national security and human rights at the Government Accountability Project, described the grim terrain that confronts whistleblowers, especially the ones charged under the Espionage Act: “When journalists become targets, they have a community and a lobby of powerful advocates to go to for support. Whistleblowers are in the wilderness…. They’re indicted under the most serious charge you can level against an American: being an enemy of the state.”

The case against Sterling has inched toward trial. In June, the Supreme Court let stand a Fourth Circuit decision that no journalist’s privilege exists covering the confidentiality of sources, a decision avidly sought by the Justice Department. The government successfully appealed an order by Judge Brinkema throwing out two of its witnesses. A pretrial conference is expected later this fall, and unless there’s a plea deal—which appears increasingly unlikely—the Sterling case will be headed to trial by spring. Risen remains resolute that he will not betray a source; it’s anyone’s guess whether that will result in his imprisonment.

If the government’s indictment is accurate in its claim that Sterling divulged classified information, then he took a great risk to inform the public about an action that, in Risen’s words, “may have been one of the most reckless operations in the modern history of the CIA.” If the indictment is false, then Sterling is guilty of nothing more than charging the agency with racial bias and going through channels to inform the Senate Intelligence Committee of extremely dangerous CIA actions. Either way, Jeffrey Sterling is now facing dire consequences as a whistleblower in the Obama era.

Take Action: Support James Risen